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The same year, Dr. Cochrane gave a commencement address at Princeton. In it he diverted from his prepared statements and started talking about "what really happened at first contact." He said that aliens had come from the future to enslave the Human race, but were stopped by a group of Humans who were also from the future. As Cochrane was known not only for his imaginative stories, as well as his frequent drinking, no one took the story seriously. He ended up recanting his statements only a few years later. (ENT: "Regeneration")

What was unknown to the public for centuries was that Cochrane's story was, in fact, very true. A Borg sphere had come back in time from the year 2373 in order to prevent Humanity's first warp flight and in turn, prevent the founding of the United Federation of Planets a century later. The sphere was pursued and subsequently destroyed by the Federation starship USS Enterprise-E, but not before a small contingent of Borg drones beamed aboard the Enterprise and began assimilating the vessel. Thanks to the efforts of the Enterprise crew, the Borg were vanquished and the flight of the Phoenix went forward as history recorded. (Star Trek: First Contact)

Ninety years later, an arctic research team uncovered the remains of the Borg sphere destroyed by the Enterprise. Also found in the debris were two frozen Borg drones, which quickly began regenerating. Not knowing the threat these two drones possessed, the research team allowed the process to go unhindered. This proved to be a critical mistake: the two drones assimilated the research team when they regained consciousness. They then stole the research team's transport and set a course for the Delta Quadrant.

Starfleet ordered Enterprise NX-01 to pursue. Enterprise caught up to the transport as it was attacking a Tarkalean freighter and quickly drove it away. Although DoctorPhlox attempted to treat the survivors, they eventually succumbed to the nanoprobes that had been injected into them during the Borg attack. CaptainJonathan Archer was forced to blow the two new drones into space when they tried to take over the ship before resuming pursuit of the Borg vessel.

Enterprise again caught up to the transport and during the subsequent battle, the transport managed to activate the program the Tarkalean drones had set up to disable the vessel. Captain Archer and his security officerLieutenantMalcolm Reed beamed over to the Borg vessel and attempted to rescue the research team, although it did not take them long to realize that this was beyond their abilities. After disabling the transport, the two officers returned to Enterprise and destroyed the transport with a full spread of photonic torpedoes, thereby ending the crisis.

Unfortunately, it was revealed that shortly before the Borg vessel was destroyed, the drones transmitted a message to their territory deep in the Delta Quadrant, with an estimated arrival time predicted for sometime in the 24th century, assuming it would arrive at all. During this incident, the Borg never identified themselves by name. Over the course of the next two centuries, this incident would be gradually forgotten as Enterprise resumed its exploratory mission and continued to pave the way for the founding of the United Federation of Planets eight years later. (ENT: "Regeneration", "These Are the Voyages...")

Over the next several decades, rumors about the existence of the Borg, mostly from El-Aurian refugees who fled their homeworld when it was assimilated around 2265 began to spread among a few Federation citizens. These rumors gave Starfleet enough cause to open a classified file on the Borg in 2293. (TNG: "Q Who"; VOY: "Scorpion", "Dark Frontier"; Star Trek Generations)

Two exobiologists prone to these rumors, Magnus and Erin Hansen, became interested in locating and studying the Borg. In 2353, they departed in the starship USS Raven with their young daughter Annika. After tracking only stray readings and sensor echos for over eight months, the Raven finally located a Borg cube. While studying the cube, the Raven was pulled into a transwarp conduit that pulled the vessel 60,000 light years into the Delta Quadrant, the Borg's native territory.

The Hansens managed to create several new technologies and strategies that allowed them to study the Borg undetected for the next two years. In 2356, the Raven was hit by an ion storm which damaged the vessels multi-adaptive shielding - which had allowed the Raven to remain undetected during the Hansens' studies. The Borg perceived the Raven as a threat following this incident, and subsequently assimilated the Hansen family. (VOY: "The Raven", "Dark Frontier")

In 2363, the Borg assimilated the USS Tombaugh, captained by Captain Blackwood, in what was apparently the first encounter between the Borg and the Federation in the 24th century. (VOY: "Infinite Regress")

In 2364, the Borg assimilated several outposts on both sides of the Romulan Neutral Zone. Neither the Federation nor the Romulans were familiar with the Borg at the time and were unable to conclusively determine who was responsible for the attacks. It was clear, however, from the level of destruction that the attack was from a species that was more powerful by far than either the Romulan Empire or the Federation. The outposts were not simply destroyed, they appeared as if some great force scooped them up from the planet surface. (TNG: "The Neutral Zone")

It was not until the following year, when the entity known as Q hurled the USS Enterprise-D 7,000 light years to a region of space assimilated by the Borg. An analysis of System J-25 found signs of an advanced civilization, but the cities appeared to have been removed in a manner identical to the loss of the Neutral Zone outposts. A Borg Cube intercepted the Enterprise and drained its shields using a tractor beam. The Enterprise responded by firing phasers at the Borg cube, causing significant damage. The Borg regenerated and repaired its hull while the Enterprise attempted to flee. Unable to outrun the Borg ship, the Enterprise fired again on the Borg Cube, but Borg had adapted to Federation weapons. Several direct photon torpedo hits had no effect on the Borg ship. Just as the Enterprise was about to be assimilated, Q returned the ship to Federation space. (TNG: "Q Who")

In 2366, a Borg Cube entered Federation space and assimilated the New Providence colony in the same manner as System J-25 and the Neutral Zone outposts. Shortly thereafter, The USS Lalo encountered the Borg Cube and reported their position shortly before it went missing. The USS Enterprise-D proceeded to the Lalo's last reported position where they exchanged fire with the Borg Cube. The Borg boarded the Enterprise and assimilated Captain Jean-Luc Picard. Now armed with Picard's tactical knowledge and experience with Starfleet, the Borg ship proceeded to Earth for the assimilation of that planet.

The Federation now considered itself in a state of war. Starfleet mobilized an armada of 40 starships led by Admiral J.P. Hanson to intercept the Borg Cube at Wolf 359. The Enterprise was unable to pursue the Borg any further due to battle damage and could not join Starfleet at the Wolf system. Hanson decided that Picard would be considered a casualty of war. The armada would use all its firepower to destroy the Borg ship. No attempt would be made to rescue the captain. The resulting Battle of Wolf 359 turned out to be a disaster. The Federation fleet was decimated. The Borg ship was undamaged. The Enterprise, finally repaired, intercepted the Borg ship and rescued Captain Picard in a daring raid. Using Picard's interface with the Borg Collective, the Enterprise was able to initiate a regeneration protocol that in essence put the Borg crew "to sleep". The Borg Cube self destructed shortly thereafter.
(TNG: "The Best of Both Worlds")

In 2368, the USS Enterprise-D encountered a crashed Borg scout ship with one survivor - a Borg drone nicknamed Hugh by the crew. The Federation still considered themselves at war with the Borg and the Enterprise developed a computer virus that could be implanted in Hugh. The virus would then spread throughout the Borg Collective until the entire collective was destroyed. However, once Hugh was isolated from the Collective, he began to shows signs of individuality. Captain Picard no longer felt justified in using a free being as an act of genocide against his own people and did not deploy the virus. Admiral Alynna Nechayev was outraged, stating that Picard's duty as a Starfleet Officer was to safeguard the lives of Federation citizens, despite whatever reservations his conscience may hold. Nechayev also ordered Picard to seize any future opportunity to destroy the Borg. (TNG: "I Borg")

When the Borg attacked the Federation outpost Ohniaka III in 2369, Captain Picard also questioned his own decision not to deploy the virus. However it was later discovered that the attack was not from the Borg Collective but rather a group of disconnected drones that were following orders from Lore. Once Lore was killed, the attacks stopped. (TNG: "Descent")

The second major battle occurred in 2373. A Borg Cube destroyed the Federation colony on Ivor Prime and was on a direct course for Earth. Admiral Hayes mobilized a Federation fleet in the Typhon sector to engage the Borg. Hayes felt that having a man who was previously captured and assimilated by the Borg on the front lines would introduce an "unstable element in a critical situation". Therefore he ordered Captain Picard to take the USS Enterprise-E on a patrol of the Neutral Zone, in case the Romulans decided to take advantage of the situation. The Federation fleet intercepted the Borg cube and opened fire in the Battle of Sector 001. The Cube quickly broke through the defense perimeter inflicting serious damage and casualties on the fleet. The Flagship sent a distress signal to Starfleet Command, requesting reinforcements. Captain Picard, hearing the distress signal, ordered the Enterprise back to Earth in violation of Hayes' orders. When the Enterprise arrived, the Federation fleet had taken heavy losses. A number of ships had been destroyed including Admiral Hayes' flagship. Many more, including the USS Defiant were severely damaged. Captain Picard took command of the fleet and used his knowledge of the Borg to determine a vulnerable point in the Borg's defenses. He ordered the fleet to target the same section and fire simultaneously. After the fleet concentrated a heavy barrage of torpedoes and phaser fire on the weak point, the Borg Cube was destroyed. (Star Trek: First Contact)

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USS Voyager had a series of skirmishes over a five-year period from 2373-2378 during which time the ship was engaged in a number of primarily defensive battles with the Borg Collective. The conflict, which would have logically been expected to be a one-sided affair between the lone Federationstarship and substantial elements of the Collective began when the Intrepid-class vessel entered Borg space in 2373. (VOY: "Scorpion")

Voyager's original plan was to by-pass Borg space in an effort to evade the Collective. However, this tactic failed and the ship engaged the Borg several times. Other than a brief alliance of convenience against the greater common threat of Species 8472, the Conflict might best be described as a series of running battles. At one juncture in that temporary period of cooperation, the Borg assigned "Seven of Nine" to represent them in council with Captain Janeway. The Captain learned from Seven that Species 8472 was only trying to prevent being being assimilated and, to that end, had launched a defensive war against the Collective. With the help of Seven of Nine, Voyager successfully escaped and made it out of Borg space. However, several Borg drones were still on Voyager including the former Human Seven of Nine.

Seven of Nine, born Annika Hansen, was taken and assimilated by the Borg Collective at the age of six. Her parents were captured along with Annika; they are presumed to be the first Earth Humans to undergo the assimilation process. Following the temporary alliance against Species 8472, Voyager left Borg space with several drones, including Seven of Nine, still on board. Despite previous agreements and cooperation, Seven of Nine and the other Borg attempted to seize the ship from Janeway. In the process, all Borg on board were killed except Seven of Nine, who was severed from the Hive mind. Her re-humanization began almost immediately: her body began to reject her Borg components and cellular structures, forcing the ship's doctor to surgically remove the Borg implants in her body and allowing her Human structures to regain control. Seven of Nine accepted her humanity and began life as a crewman aboard Voyager, greatly affecting the outcome of the ship's future encounters with the Borg and boosting the crew's confidence in their ability to fight the Collective despite the unfavorable odds.

With Seven of Nine a crew member, the former drone helped the Voyager crew even the odds in future encounters with the Borg by using her extensive knowledge and residual Borg technology. She partially assimilated portions of Voyager, including major ship's systems; the hybrid technology proved to be much more efficient. She also helped to create weapons that countered the ability of Borg drones to adapt to Federation firepower.

After learning of a Borg sphere that was heavily damaged, Voyager and her crew launched a mission to infiltrate the sphere and retrieve a transwarp coil to try to shave years off Voyager's trip. The crew succeeded in retrieving the coil, using bio-dampeners and multi-adaptive shielding devised by Seven's parents to remain undetected, but Seven of Nine was contacted by the Borg Queen who offered her Voyager's safety in exchange for her rejoining the Collective. Her plan was to use Seven and her experience to successfully assimilate humanity and not turn her back into a normal drone again. She makes her watch as the Borg assimilates another species, but Seven helps four prisoners escape. The Queen detects this and prepares to capture them again, but Seven pleads with her to let them go which the Queen does for some reason. Using the transwarp coil, Captain Janeway, Tuvok, The Doctor and Tom Paris follow the sphere to the Unicomplex in the Delta Flyer where they effect a rescue of Seven. As the Queen's chambers are too heavily shielded to beam Seven out, Janeway and Tuvok beam in to the complex to lower the shields. Also, Janeway has The Doctor contact Seven which strengthens her faltering resolve, but causes the Borg Queen to detect the team's presence. As she has assimilated the Hansens, the Queen has assimilated their shielding technology and sends three Borg cubes after the Delta Flyer, penetrating its shields. The Flyer keeps remodulating the shielding to become invisible again but the Borg each time. In the corridors, force fields prevent Janeway and Tuvok from moving, but seeing that Borg drones can get through, Janeway uses a drone to determine the field's frequency and modulates her bio-dampner to pass through it. This works, but her bio-dampner shorts out, leaving her visible to the Borg sensors. Janeway sends Tuvok to lower the shielding while she rescues Seven. Janeway reaches the Queen's chambers as she prepares to re-assimilate Seven and threatens to kill the Queen if she doesn't call off the drones in the room and the cubes. To demonstrate her resolve, Janeway has the Flyer fire on the room and the Queen gives in. Tuvok successfully lowers the shields and Janeway orders beam-out, but the Queen puts up a dispersal field to prevent this. Janeway orders Seven to lower the field while the Queen orders her not to. Choosing Voyager over the Borg, Seven lowers the field, but the Queen raises it again. Seven senses through her restored link to the Collective that if the power node over the Queen is destroyed, it will disrupt her control over the field and drop it again. She informs Janeway of this and she shoots the node, causing the field to go down and allowing the Flyer to beam her, Seven and Tuvok out of the complex. The Flyer flees, chased by the cubes and the Borg Queen's vessel. When it jumps to transwarp, only the Queen's ship follows. The Flyer takes damage, but manages to make it back to Voyager which fires a spread of photon torpedos, collapsing the corridor for a light-year and destroying the Borg vessel. Voyager is then able to use the transwarp coil to travel 20,000 light years before it burns out, shaving another 15 years off their journey.

Within the Collective a virus broke out, creating a shared virtual reality known as Unimatrix Zero in which Borg drones were able to become individuals again. Years prior for Seven of Nine being liberated from the collective she too lived in Unimatrix zero and was romantically involved with another drone named Axum. The Borg Queen was initially unable to detect the virus; over several years it spread among thousands of Borg. The Borg Queen immediately began deactivating drones in order to contain and destroy the virus, but Axum was able to contact Seven and ask her to help him and the former drones. Seven reported this information to Captain Janeway and, using a mind-meld performed by Commander Tuvok, Janeway was able to enter Unimatrix Zero; within the construct the Starship Captain and the infected drones developed and instigated the plan for a resistance movement against the Borg Collective.
The Borg Queen did eventually uncover the plans and initiated a strategy to stop the rebellion. She visited Unimatrix herself to witness it first hand. Unimatrix Zero was destroyed, but Voyager's crew was able to come up with a way to allow the drones to retain their individuality outside and Axum began a rebellion against the Queen.

In an alternate future, Kathryn Janeway developed substantial technology with which to fight the Borg including ablative armor and transphasic torpedos. When she comes back in time to change history, she brings these technologies with her on her shuttlecraft SC-4 and equips Voyager with them. Using the new technology, Admiral Janeway leads Voyager to a Borg transwarp hub through which they can return to the Alpha Quadrant using one of the hub's transwarp conduits. After her cubes prove to be no match for the improved Voyager, the Borg Queen calls them off, deciding to allow Voyager to pass rather than risk more ships to stop it. However, upon learning what the hub is, Captain Janeway calls off the attempt and decides to destroy the hub instead to deliver the Borg a crippling blow, even though due to the Queen's control over its shielding and the Borg's adaptivity, it will ruin their chance to get home. Coming up with a plan, the two Janeway's come up with a way to do both: Admiral Janeway travels to the Unicomplex in her ship and uses a neural interface to interact with the Queen and offer her her technology in exchange for the Queen sending a cube to tow Voyager back to the Alpha Quadrant. While the Queen understands the Admiral's desire to protect her "Collective," she distracts her long enough for the Borg to locate her ship and capture her. Admiral Janeway is beamed directly to the Queen's chambers where the Queen personally assimilates her. However, the Admiral had injected herself with a Neurolytic pathogen which infects the Collective with her assimilation and the Borg are unable to stop it and the Queen starts to fall apart. Voyager enters the conduit leading to the Alpha Quadrant and after detecting that the shields are disrupted, destroys the hub, keeping ahead of the destruction. The Queen detects that Borg sphere634 is still able to hear her commands and sends it after Voyager with the intention to destroy Voyager as with Captain Janeway dead, Admiral Janeway and her pathogen will never exist and thus the Borg will be unaffected. Also, when the Admiral was assimilated, the Borg assimilated her knowledge about the technology she equipped Voyager with, allowing them to adapt to it and giving them an advantage. As the Queen dies, she causes the Unicomplex to self-destruct in an attempt to prevent the pathogen from spreading. Voyager is chased by the sphere and loses its armor rapidly and won't make it back to the Alpha Quadrant in one piece. The sphere opens its docking bay to try to capture Voyager as Captain Janeway orders a course change as they approach the nearest exit which leads back into the Delta Quadrant. At Earth, the Transwarp aperture the conduit comes out at open less than a light-year for Earth and 18 ships are sent to intercept. The sphere emerges alone and the fleet opens fire on it to no avail. However, Voyager landed in its docking bay and fires a torpedo, destroying the ship from the inside. Voyager emerges unharmed from the explosion, having finally made it home and having dealt the Borg a crippling blow with the destruction of the transwarp network, the Unicomplex and the Queen.